title: Energetics of Z-DNA binding protein-mediated helicity reversals in DNA, RNA, and DNA-RNA duplexes.
abstract: Z-DNA binding proteins (ZBPs) specifically recognize and stabilize left-handed double helices, including Z-DNA and Z-RNA. However, the energetics of Z-form stabilization by ZBPs have never been characterized due to the technical limitations of bulk studies, resulting in an unclear understanding of the ZBP operational mechanism at the molecular level. Here, we use single-molecule fluorescence resonance energy transfer (FRET) to determine the energetics of Z-form stabilization by ZBP for DNA, RNA, and DNA-RNA duplexes, revealing that the formation of B-Z or A-Z junctions dominates the thermodynamics and kinetics of Z-form stabilization. Furthermore, in contrast to general assumptions, the Z-form is most efficiently and most rapidly formed in the DNA-RNA hybrid duplex due to the greatly reduced junction energy in the DNA-RNA hybrid.
authors.affiliation: Department of Physics and Astronomy, ‡National Center for Creative Research Initiatives, and §Department of Biophysics and Chemical Biology, Seoul National University , Seoul 151-747, Korea.
authors.forename: Sangsu
authors.initials: S
authors.lastname: Bae
authors.forename: Yuyoung
authors.initials: Y
authors.lastname: Kim
authors.forename: Doyoun
authors.initials: D
authors.lastname: Kim
authors.forename: Kyeong Kyu
authors.initials: KK
authors.lastname: Kim
authors.forename: Yang-Gyun
authors.initials: YG
authors.lastname: Kim
authors.forename: Sungchul
authors.initials: S
authors.lastname: Hohng
mesh_terms: D043542:DNA, Z-Form / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D031541:Fluorescence Resonance Energy Transfer; D007700:Kinetics; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D043542:DNA, Z-Form; D004268:DNA-Binding Proteins; D012313:RNA